diff --git a/src/mol-script/language/expression-formatter.ts b/src/mol-script/language/expression-formatter.ts
index fda92b8c24a12a8c1fe715941f60960ee250db0b..93c1aa0366d0acd8ab5a35cd86527f4168ec4ae5 100644
--- a/src/mol-script/language/expression-formatter.ts
+++ b/src/mol-script/language/expression-formatter.ts
@@ -8,12 +8,6 @@ import Expression from './expression'
const { isLiteral, isSymbol, isArgumentsArray } = Expression;
-export default function format(e: Expression) {
- const writer = new Writer();
- _format(e, writer);
- return writer.getStr();
-}
-
class Writer {
private value: string[] = [];
private currentLineLength = 0;
@@ -128,4 +122,10 @@ function _format(e: Expression, writer: Writer) {
_format(e.args[a], writer);
}
writer.pop();
-}
\ No newline at end of file
+}
+
+export function formatMolScript(e: Expression) {
+ const writer = new Writer();
+ _format(e, writer);
+ return writer.getStr();
+}
diff --git a/src/mol-script/language/expression.ts b/src/mol-script/language/expression.ts
index d243dff0cdc3f922ca71461ee4748d11a9a62201..8fe5ac9b11f9ff1e3e4e4f810d0a3dfeec5521c3 100644
--- a/src/mol-script/language/expression.ts
+++ b/src/mol-script/language/expression.ts
@@ -20,7 +20,7 @@ namespace Expression {
export function isArgumentsArray(e?: Arguments): e is Expression[] { return !!e && Array.isArray(e); }
export function isArgumentsMap(e?: Arguments): e is { [name: string]: Expression } { return !!e && !Array.isArray(e); }
- export function isLiteral(e: Expression): e is Expression.Literal { return !isApply(e); }
+ export function isLiteral(e: Expression): e is Expression.Literal { return !isApply(e) && !isSymbol(e); }
export function isApply(e: Expression): e is Expression.Apply { return !!e && !!(e as Expression.Apply).head && typeof e === 'object'; }
export function isSymbol(e: Expression): e is Expression.Symbol { return !!e && typeof (e as any).name === 'string' }
}
diff --git a/src/mol-script/runtime/query/compiler.ts b/src/mol-script/runtime/query/compiler.ts
index 14eb9fb7bdd330c37f655115f1d94a7b585e6336..9edd815867d9d7106ab91f02beaeb9e04084f4db 100644
--- a/src/mol-script/runtime/query/compiler.ts
+++ b/src/mol-script/runtime/query/compiler.ts
@@ -134,8 +134,10 @@ function _compile(ctx: QueryCompilerCtx, expression: Expression): CompiledQueryF
}
if (Expression.isSymbol(expression)) {
- // TODO: check for "nullary symbols" and automatically apply them?
- return CompiledQueryFn.Const(expression.name);
+ const runtime = ctx.table.getRuntime(expression.name);
+ if (!runtime) return CompiledQueryFn.Const(expression.name);
+
+ return runtime.compile(ctx);
}
if (!Expression.isSymbol(expression.head)) {
@@ -143,7 +145,6 @@ function _compile(ctx: QueryCompilerCtx, expression: Expression): CompiledQueryF
}
const compiler = ctx.table.getRuntime(expression.head.name);
-
if (!compiler) {
throw new Error(`Symbol '${expression.head.name}' is not implemented.`);
}
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 70b7028af1c6175845a7ae0b2b18f509ff6237f3..245e543e0441b163187afd4e919829d254ef6b6e 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -1,300 +1,347 @@
-// /**
-// * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
-// *
-// * @author David Sehnal <david.sehnal@gmail.com>
-// */
-
-// import { MSymbol, Arguments, Argument } from '../../language/symbol'
-// import B from '../../language/builder'
-// import * as M from './macro'
-// import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table'
-// import Type from '../../language/type'
-// import * as Struct from '../../language/symbol-table/structure-query'
-// import Expression from '../../language/expression'
-// import { UniqueArray } from 'mol-data/generic'
-
-// export type MolScriptSymbol =
-// | { kind: 'alias', aliases: string[], symbol: MSymbol }
-// | { kind: 'macro', aliases: string[], symbol: MSymbol, translate: (args: any) => Expression }
-
-// function Alias(symbol: MSymbol<any>, ...aliases: string[]): MolScriptSymbol { return { kind: 'alias', aliases, symbol }; }
+/**
+ * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MSymbol, Arguments, Argument } from '../../language/symbol'
+import { MolScriptBuilder as B } from '../../language/builder'
+//import * as M from './macro'
+import { MolScriptSymbolTable as MolScript } from '../../language/symbol-table'
+import Type from '../../language/type'
+import * as Struct from '../../language/symbol-table/structure-query'
+import Expression from '../../language/expression'
+import { UniqueArray } from 'mol-data/generic'
+
+export type MolScriptSymbol =
+ | { kind: 'alias', aliases: string[], symbol: MSymbol }
+ | { kind: 'macro', aliases: string[], symbol: MSymbol, translate: (args: any) => Expression }
+
+function Alias(symbol: MSymbol<any>, ...aliases: string[]): MolScriptSymbol { return { kind: 'alias', aliases, symbol }; }
// function Macro(symbol: MSymbol<any>, translate: (args: any) => Expression, ...aliases: string[]): MolScriptSymbol {
// symbol.info.namespace = 'molscript-macro';
// symbol.id = `molscript-macro.${symbol.info.name}`;
// return { kind: 'macro', symbol, translate, aliases: [symbol.info.name, ...aliases] };
// }
-// export function isMolScriptSymbol(x: any): x is MolScriptSymbol {
-// return x.kind === 'alias' || x.kind === 'macro';
-// }
+export function isMolScriptSymbol(x: any): x is MolScriptSymbol {
+ return x.kind === 'alias' || x.kind === 'macro';
+}
-// export const SymbolTable = [
-// [
-// 'Core symbols',
-// Alias(MolScript.core.type.bool, 'bool'),
-// Alias(MolScript.core.type.num, 'num'),
-// Alias(MolScript.core.type.str, 'str'),
-// Alias(MolScript.core.type.regex, 'regex'),
-// Alias(MolScript.core.type.list, 'list'),
-// Alias(MolScript.core.type.set, 'set'),
-
-// Alias(MolScript.core.type.compositeKey, 'composite-key'),
-// Alias(MolScript.core.logic.not, 'not'),
-// Alias(MolScript.core.logic.and, 'and'),
-// Alias(MolScript.core.logic.or, 'or'),
-// Alias(MolScript.core.ctrl.if, 'if'),
-// Alias(MolScript.core.ctrl.fn, 'fn'),
-// Alias(MolScript.core.ctrl.eval, 'eval'),
-// Alias(MolScript.core.math.add, 'add', '+'),
-// Alias(MolScript.core.math.sub, 'sub', '-'),
-// Alias(MolScript.core.math.mult, 'mult', '*'),
-// Alias(MolScript.core.math.div, 'div', '/'),
-// Alias(MolScript.core.math.pow, 'pow', '**'),
-// Alias(MolScript.core.math.mod, 'mod'),
-// Alias(MolScript.core.math.min, 'min'),
-// Alias(MolScript.core.math.max, 'max'),
-// Alias(MolScript.core.math.floor, 'floor'),
-// Alias(MolScript.core.math.ceil, 'ceil'),
-// Alias(MolScript.core.math.roundInt, 'round'),
-// Alias(MolScript.core.math.abs, 'abs'),
-// Alias(MolScript.core.math.sqrt, 'sqrt'),
-// Alias(MolScript.core.math.sin, 'sin'),
-// Alias(MolScript.core.math.cos, 'cos'),
-// Alias(MolScript.core.math.tan, 'tan'),
-// Alias(MolScript.core.math.asin, 'asin'),
-// Alias(MolScript.core.math.acos, 'acos'),
-// Alias(MolScript.core.math.atan, 'atan'),
-// Alias(MolScript.core.math.sinh, 'sinh'),
-// Alias(MolScript.core.math.cosh, 'cosh'),
-// Alias(MolScript.core.math.tanh, 'tanh'),
-// Alias(MolScript.core.math.exp, 'exp'),
-// Alias(MolScript.core.math.log, 'log'),
-// Alias(MolScript.core.math.log10, 'log10'),
-// Alias(MolScript.core.math.atan2, 'atan2'),
-// Alias(MolScript.core.rel.eq, 'eq', '='),
-// Alias(MolScript.core.rel.neq, 'neq', '!='),
-// Alias(MolScript.core.rel.lt, 'lt', '<'),
-// Alias(MolScript.core.rel.lte, 'lte', '<='),
-// Alias(MolScript.core.rel.gr, 'gr', '>'),
-// Alias(MolScript.core.rel.gre, 'gre', '>='),
-// Alias(MolScript.core.rel.inRange, 'in-range'),
-// Alias(MolScript.core.str.concat, 'concat'),
-// Alias(MolScript.core.str.match, 'regex.match'),
-// Alias(MolScript.core.list.getAt, 'list.get'),
-// Alias(MolScript.core.set.has, 'set.has'),
-// Alias(MolScript.core.set.isSubset, 'set.subset'),
-// ],
-// [
-// 'Structure',
-// [
-// 'Types',
-// Alias(MolScript.structureQuery.type.entityType, 'ent-type'),
-// Alias(MolScript.structureQuery.type.authResidueId, 'auth-resid'),
-// Alias(MolScript.structureQuery.type.labelResidueId, 'label-resid'),
-// Alias(MolScript.structureQuery.type.ringFingerprint, 'ringfp'),
-// Alias(MolScript.structureQuery.type.bondFlags, 'bond-flags'),
-// ],
-// [
-// 'Slots',
-// Alias(MolScript.structureQuery.slot.elementSetReduce, 'atom.set.reduce.value'),
-// ],
-// [
-// 'Generators',
-// Alias(MolScript.structureQuery.generator.atomGroups, 'sel.atom.atom-groups'),
-// Alias(MolScript.structureQuery.generator.queryInSelection, 'sel.atom.query-in-selection'),
-// Alias(MolScript.structureQuery.generator.rings, 'sel.atom.rings'),
-// Alias(MolScript.structureQuery.generator.empty, 'sel.atom.empty'),
-
-// Macro(MSymbol('sel.atom.atoms', Arguments.Dictionary({
-// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to each atom.' })
-// }), Struct.Types.ElementSelection, 'A selection of singleton atom sets.'),
-// args => B.struct.generator.atomGroups({ 'atom-test': M.tryGetArg(args, 0, true) })),
-
-// Macro(MSymbol('sel.atom.res', Arguments.Dictionary({
-// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each residue.' })
-// }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by residue.'),
-// args => B.struct.generator.atomGroups({
-// 'residue-test': M.tryGetArg(args, 0, true),
-// 'group-by': B.ammp('residueKey')
-// })),
-
-// Macro(MSymbol('sel.atom.chains', Arguments.Dictionary({
-// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
-// }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by chain.'),
-// args => B.struct.generator.atomGroups({
-// 'chain-test': M.tryGetArg(args, 0, true),
-// 'group-by': B.ammp('chainKey')
-// })),
-// ],
-// [
-// 'Modifiers',
-// Alias(MolScript.structureQuery.modifier.queryEach, 'sel.atom.query-each'),
-// Alias(MolScript.structureQuery.modifier.intersectBy, 'sel.atom.intersect-by'),
-// Alias(MolScript.structureQuery.modifier.exceptBy, 'sel.atom.except-by'),
-// Alias(MolScript.structureQuery.modifier.unionBy, 'sel.atom.union-by'),
-// Alias(MolScript.structureQuery.modifier.union, 'sel.atom.union'),
-// Alias(MolScript.structureQuery.modifier.cluster, 'sel.atom.cluster'),
-// Alias(MolScript.structureQuery.modifier.includeSurroundings, 'sel.atom.include-surroundings'),
-// Alias(MolScript.structureQuery.modifier.includeConnected, 'sel.atom.include-connected'),
-// Alias(MolScript.structureQuery.modifier.expandProperty, 'sel.atom.expand-property'),
-
-// Macro(MSymbol('sel.atom.around', Arguments.Dictionary({
-// 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
-// }), Struct.Types.ElementSelection, 'A selection of singleton atom sets with centers within "radius" of the center of any atom in the given selection.'),
-// args => B.struct.modifier.exceptBy({
-// '0': B.struct.filter.within({
-// '0': B.struct.generator.atomGroups(), target: M.tryGetArg(args, 0), 'max-radius': M.tryGetArg(args, 'radius')
-// }),
-// by: M.tryGetArg(args, 0)
-// }))
-// ],
-// [
-// 'Filters',
-// Alias(MolScript.structureQuery.filter.pick, 'sel.atom.pick'),
-// Alias(MolScript.structureQuery.filter.withSameAtomProperties, 'sel.atom.with-same-atom-properties'),
-// Alias(MolScript.structureQuery.filter.intersectedBy, 'sel.atom.intersected-by'),
-// Alias(MolScript.structureQuery.filter.within, 'sel.atom.within'),
-// Alias(MolScript.structureQuery.filter.isConnectedTo, 'sel.atom.is-connected-to'),
-// ],
-// [
-// 'Combinators',
-// Alias(MolScript.structureQuery.combinator.intersect, 'sel.atom.intersect'),
-// Alias(MolScript.structureQuery.combinator.merge, 'sel.atom.merge'),
-// Alias(MolScript.structureQuery.combinator.distanceCluster, 'sel.atom.dist-cluster'),
-// ],
-// [
-// 'Atom Set Properties',
-// Alias(MolScript.structureQuery.atomSet.atomCount, 'atom.set.atom-count'),
-// Alias(MolScript.structureQuery.atomSet.countQuery, 'atom.set.count-query'),
-// Alias(MolScript.structureQuery.atomSet.reduce, 'atom.set.reduce'),
-// Alias(MolScript.structureQuery.atomSet.propertySet, 'atom.set.property'),
-
-// Macro(MSymbol('atom.set.max', Arguments.Dictionary({
-// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
-// }), Type.Num, 'Maximum of the given property in the current atom set.'),
-// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.max)),
-
-// Macro(MSymbol('atom.set.sum', Arguments.Dictionary({
-// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
-// }), Type.Num, 'Sum of the given property in the current atom set.'),
-// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0)),
-
-// Macro(MSymbol('atom.set.avg', Arguments.Dictionary({
-// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
-// }), Type.Num, 'Average of the given property in the current atom set.'),
-// args => B.core.math.div([ M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0), B.struct.atomSet.atomCount() ])),
-
-// Macro(MSymbol('atom.set.min', Arguments.Dictionary({
-// 0: Argument(Type.Num, { description: 'Numeric atom property.'})
-// }), Type.Num, 'Minimum of the given property in the current atom set.'),
-// args => M.aggregate(M.tryGetArg(args, 0), B.core.math.min))
-// ],
-// [
-// 'Atom Properties',
-// Alias(MolScript.structureQuery.atomProperty.core.elementSymbol, 'atom.el'),
-// Alias(MolScript.structureQuery.atomProperty.core.vdw, 'atom.vdw'),
-// Alias(MolScript.structureQuery.atomProperty.core.mass, 'atom.mass'),
-// Alias(MolScript.structureQuery.atomProperty.core.atomicNumber, 'atom.atomic-number'),
-// Alias(MolScript.structureQuery.atomProperty.core.x, 'atom.x'),
-// Alias(MolScript.structureQuery.atomProperty.core.y, 'atom.y'),
-// Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
-// Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
-// Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
-
-// Alias(MolScript.structureQuery.atomProperty.topology.connectedComponentKey, 'atom.key.molecule'),
-
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.authResidueId, 'atom.auth-resid'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.labelResidueId, 'atom.label-resid'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.residueKey, 'atom.key.res'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.chainKey, 'atom.key.chain'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.entityKey, 'atom.key.entity'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.isHet, 'atom.is-het'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.id, 'atom.id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_atom_id, 'atom.label_atom_id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_alt_id, 'atom.label_alt_id', 'atom.altloc'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_comp_id, 'atom.label_comp_id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_asym_id, 'atom.label_asym_id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_entity_id, 'atom.label_entity_id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.label_seq_id, 'atom.label_seq_id'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_atom_id, 'atom.auth_atom_id', 'atom.name'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_comp_id, 'atom.auth_comp_id', 'atom.resname'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_asym_id, 'atom.auth_asym_id', 'atom.chain'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_seq_id, 'atom.auth_seq_id', 'atom.resno'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_PDB_ins_code, 'atom.pdbx_PDB_ins_code', 'atom.inscode'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_formal_charge, 'atom.pdbx_formal_charge'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.occupancy, 'atom.occupancy'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
-
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, 'atom.key.sec-struct'),
-
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.isModified, 'atom.is-modified'),
-// Alias(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, 'atom.modified-parent'),
-
-// Macro(MSymbol('atom.sec-struct.is', Arguments.List(Struct.Types.SecondaryStructureFlag), Type.Bool,
-// `Test if the current atom is part of an secondary structure. Optionally specify allowed sec. struct. types: ${Type.oneOfValues(Struct.Types.SecondaryStructureFlag).join(', ')}`),
-// args => B.core.flags.hasAny([B.struct.atomProperty.macromolecular.secondaryStructureFlags(), B.struct.type.secondaryStructureFlags(args)])),
-// ],
-// [
-// 'Bond Properties',
-// Alias(MolScript.structureQuery.bondProperty.order, 'bond.order'),
-// Macro(MSymbol('bond.is', Arguments.List(Struct.Types.BondFlag), Type.Bool,
-// `Test if the current bond has at least one (or all if partial = false) of the specified flags: ${Type.oneOfValues(Struct.Types.BondFlag).join(', ')}`),
-// args => B.core.flags.hasAny([B.struct.bondProperty.flags(), B.struct.type.bondFlags(M.getPositionalArgs(args))])),
-// ]
-// ]
-// ];
-
-// const list: MolScriptSymbol[] = [];
-
-// function makeList(xs: any[]) {
-// for (const x of xs) {
-// if (isMolScriptSymbol(x)) list.push(x);
-// else if (x instanceof Array) makeList(x);
-// }
-// }
+export const SymbolTable = [
+ [
+ 'Core symbols',
+ Alias(MolScript.core.type.bool, 'bool'),
+ Alias(MolScript.core.type.num, 'num'),
+ Alias(MolScript.core.type.str, 'str'),
+ Alias(MolScript.core.type.regex, 'regex'),
+ Alias(MolScript.core.type.list, 'list'),
+ Alias(MolScript.core.type.set, 'set'),
+
+ Alias(MolScript.core.type.compositeKey, 'composite-key'),
+ Alias(MolScript.core.logic.not, 'not'),
+ Alias(MolScript.core.logic.and, 'and'),
+ Alias(MolScript.core.logic.or, 'or'),
+ Alias(MolScript.core.ctrl.if, 'if'),
+ Alias(MolScript.core.ctrl.fn, 'fn'),
+ Alias(MolScript.core.ctrl.eval, 'eval'),
+ Alias(MolScript.core.math.add, 'add', '+'),
+ Alias(MolScript.core.math.sub, 'sub', '-'),
+ Alias(MolScript.core.math.mult, 'mult', '*'),
+ Alias(MolScript.core.math.div, 'div', '/'),
+ Alias(MolScript.core.math.pow, 'pow', '**'),
+ Alias(MolScript.core.math.mod, 'mod'),
+ Alias(MolScript.core.math.min, 'min'),
+ Alias(MolScript.core.math.max, 'max'),
+ Alias(MolScript.core.math.floor, 'floor'),
+ Alias(MolScript.core.math.ceil, 'ceil'),
+ Alias(MolScript.core.math.roundInt, 'round'),
+ Alias(MolScript.core.math.abs, 'abs'),
+ Alias(MolScript.core.math.sqrt, 'sqrt'),
+ Alias(MolScript.core.math.sin, 'sin'),
+ Alias(MolScript.core.math.cos, 'cos'),
+ Alias(MolScript.core.math.tan, 'tan'),
+ Alias(MolScript.core.math.asin, 'asin'),
+ Alias(MolScript.core.math.acos, 'acos'),
+ Alias(MolScript.core.math.atan, 'atan'),
+ Alias(MolScript.core.math.sinh, 'sinh'),
+ Alias(MolScript.core.math.cosh, 'cosh'),
+ Alias(MolScript.core.math.tanh, 'tanh'),
+ Alias(MolScript.core.math.exp, 'exp'),
+ Alias(MolScript.core.math.log, 'log'),
+ Alias(MolScript.core.math.log10, 'log10'),
+ Alias(MolScript.core.math.atan2, 'atan2'),
+ Alias(MolScript.core.rel.eq, 'eq', '='),
+ Alias(MolScript.core.rel.neq, 'neq', '!='),
+ Alias(MolScript.core.rel.lt, 'lt', '<'),
+ Alias(MolScript.core.rel.lte, 'lte', '<='),
+ Alias(MolScript.core.rel.gr, 'gr', '>'),
+ Alias(MolScript.core.rel.gre, 'gre', '>='),
+ Alias(MolScript.core.rel.inRange, 'in-range'),
+ Alias(MolScript.core.str.concat, 'concat'),
+ Alias(MolScript.core.str.match, 'regex.match'),
+ Alias(MolScript.core.list.getAt, 'list.get'),
+ Alias(MolScript.core.set.has, 'set.has'),
+ Alias(MolScript.core.set.isSubset, 'set.subset'),
+ ],
+ [
+ 'Structure',
+ [
+ 'Types',
+ Alias(MolScript.structureQuery.type.entityType, 'ent-type'),
+ Alias(MolScript.structureQuery.type.authResidueId, 'auth-resid'),
+ Alias(MolScript.structureQuery.type.labelResidueId, 'label-resid'),
+ Alias(MolScript.structureQuery.type.ringFingerprint, 'ringfp'),
+ Alias(MolScript.structureQuery.type.bondFlags, 'bond-flags'),
+ ],
+ [
+ 'Slots',
+ Alias(MolScript.structureQuery.slot.elementSetReduce, 'atom.set.reduce.value'),
+ ],
+ [
+ 'Generators',
+ Alias(MolScript.structureQuery.generator.atomGroups, 'sel.atom.atom-groups'),
+ Alias(MolScript.structureQuery.generator.queryInSelection, 'sel.atom.query-in-selection'),
+ Alias(MolScript.structureQuery.generator.rings, 'sel.atom.rings'),
+ Alias(MolScript.structureQuery.generator.empty, 'sel.atom.empty'),
+
+ // Macro(MSymbol('sel.atom.atoms', Arguments.Dictionary({
+ // 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to each atom.' })
+ // }), Struct.Types.ElementSelection, 'A selection of singleton atom sets.'),
+ // args => B.struct.generator.atomGroups({ 'atom-test': M.tryGetArg(args, 0, true) })),
+
+ // Macro(MSymbol('sel.atom.res', Arguments.Dictionary({
+ // 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each residue.' })
+ // }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by residue.'),
+ // args => B.struct.generator.atomGroups({
+ // 'residue-test': M.tryGetArg(args, 0, true),
+ // 'group-by': B.ammp('residueKey')
+ // })),
+
+ // Macro(MSymbol('sel.atom.chains', Arguments.Dictionary({
+ // 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
+ // }), Struct.Types.ElementSelection, 'A selection of atom sets grouped by chain.'),
+ // args => B.struct.generator.atomGroups({
+ // 'chain-test': M.tryGetArg(args, 0, true),
+ // 'group-by': B.ammp('chainKey')
+ // })),
+ ],
+ [
+ 'Modifiers',
+ Alias(MolScript.structureQuery.modifier.queryEach, 'sel.atom.query-each'),
+ Alias(MolScript.structureQuery.modifier.intersectBy, 'sel.atom.intersect-by'),
+ Alias(MolScript.structureQuery.modifier.exceptBy, 'sel.atom.except-by'),
+ Alias(MolScript.structureQuery.modifier.unionBy, 'sel.atom.union-by'),
+ Alias(MolScript.structureQuery.modifier.union, 'sel.atom.union'),
+ Alias(MolScript.structureQuery.modifier.cluster, 'sel.atom.cluster'),
+ Alias(MolScript.structureQuery.modifier.includeSurroundings, 'sel.atom.include-surroundings'),
+ Alias(MolScript.structureQuery.modifier.includeConnected, 'sel.atom.include-connected'),
+ Alias(MolScript.structureQuery.modifier.expandProperty, 'sel.atom.expand-property'),
+
+ // Macro(MSymbol('sel.atom.around', Arguments.Dictionary({
+ // 0: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test applied to the 1st atom of each chain.' })
+ // }), Struct.Types.ElementSelection, 'A selection of singleton atom sets with centers within "radius" of the center of any atom in the given selection.'),
+ // args => B.struct.modifier.exceptBy({
+ // '0': B.struct.filter.within({
+ // '0': B.struct.generator.atomGroups(), target: M.tryGetArg(args, 0), 'max-radius': M.tryGetArg(args, 'radius')
+ // }),
+ // by: M.tryGetArg(args, 0)
+ // }))
+ ],
+ [
+ 'Filters',
+ Alias(MolScript.structureQuery.filter.pick, 'sel.atom.pick'),
+ Alias(MolScript.structureQuery.filter.withSameAtomProperties, 'sel.atom.with-same-atom-properties'),
+ Alias(MolScript.structureQuery.filter.intersectedBy, 'sel.atom.intersected-by'),
+ Alias(MolScript.structureQuery.filter.within, 'sel.atom.within'),
+ Alias(MolScript.structureQuery.filter.isConnectedTo, 'sel.atom.is-connected-to'),
+ ],
+ [
+ 'Combinators',
+ Alias(MolScript.structureQuery.combinator.intersect, 'sel.atom.intersect'),
+ Alias(MolScript.structureQuery.combinator.merge, 'sel.atom.merge'),
+ Alias(MolScript.structureQuery.combinator.distanceCluster, 'sel.atom.dist-cluster'),
+ ],
+ [
+ 'Atom Set Properties',
+ Alias(MolScript.structureQuery.atomSet.atomCount, 'atom.set.atom-count'),
+ Alias(MolScript.structureQuery.atomSet.countQuery, 'atom.set.count-query'),
+ Alias(MolScript.structureQuery.atomSet.reduce, 'atom.set.reduce'),
+ Alias(MolScript.structureQuery.atomSet.propertySet, 'atom.set.property'),
+
+ // Macro(MSymbol('atom.set.max', Arguments.Dictionary({
+ // 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+ // }), Type.Num, 'Maximum of the given property in the current atom set.'),
+ // args => M.aggregate(M.tryGetArg(args, 0), B.core.math.max)),
+
+ // Macro(MSymbol('atom.set.sum', Arguments.Dictionary({
+ // 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+ // }), Type.Num, 'Sum of the given property in the current atom set.'),
+ // args => M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0)),
+
+ // Macro(MSymbol('atom.set.avg', Arguments.Dictionary({
+ // 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+ // }), Type.Num, 'Average of the given property in the current atom set.'),
+ // args => B.core.math.div([ M.aggregate(M.tryGetArg(args, 0), B.core.math.add, 0), B.struct.atomSet.atomCount() ])),
+
+ // Macro(MSymbol('atom.set.min', Arguments.Dictionary({
+ // 0: Argument(Type.Num, { description: 'Numeric atom property.'})
+ // }), Type.Num, 'Minimum of the given property in the current atom set.'),
+ // args => M.aggregate(M.tryGetArg(args, 0), B.core.math.min))
+ ],
+ [
+ 'Atom Properties',
+ Alias(MolScript.structureQuery.atomProperty.core.elementSymbol, 'atom.el'),
+ Alias(MolScript.structureQuery.atomProperty.core.vdw, 'atom.vdw'),
+ Alias(MolScript.structureQuery.atomProperty.core.mass, 'atom.mass'),
+ Alias(MolScript.structureQuery.atomProperty.core.atomicNumber, 'atom.atomic-number'),
+ Alias(MolScript.structureQuery.atomProperty.core.x, 'atom.x'),
+ Alias(MolScript.structureQuery.atomProperty.core.y, 'atom.y'),
+ Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
+ Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
+ Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
+
+ Alias(MolScript.structureQuery.atomProperty.topology.connectedComponentKey, 'atom.key.molecule'),
+
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.authResidueId, 'atom.auth-resid'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.labelResidueId, 'atom.label-resid'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.residueKey, 'atom.key.res'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.chainKey, 'atom.key.chain'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.entityKey, 'atom.key.entity'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.isHet, 'atom.is-het'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.id, 'atom.id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_atom_id, 'atom.label_atom_id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_alt_id, 'atom.label_alt_id', 'atom.altloc'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_comp_id, 'atom.label_comp_id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_asym_id, 'atom.label_asym_id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_entity_id, 'atom.label_entity_id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.label_seq_id, 'atom.label_seq_id'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_atom_id, 'atom.auth_atom_id', 'atom.name'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_comp_id, 'atom.auth_comp_id', 'atom.resname'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_asym_id, 'atom.auth_asym_id', 'atom.chain'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.auth_seq_id, 'atom.auth_seq_id', 'atom.resno'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_PDB_ins_code, 'atom.pdbx_PDB_ins_code', 'atom.inscode'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.pdbx_formal_charge, 'atom.pdbx_formal_charge'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.occupancy, 'atom.occupancy'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.B_iso_or_equiv, 'atom.B_iso_or_equiv', 'atom.bfactor'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.entityType, 'atom.entity-type'),
+
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureKey, 'atom.key.sec-struct'),
+
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.isModified, 'atom.is-modified'),
+ Alias(MolScript.structureQuery.atomProperty.macromolecular.modifiedParentName, 'atom.modified-parent'),
+
+ // Macro(MSymbol('atom.sec-struct.is', Arguments.List(Struct.Types.SecondaryStructureFlag), Type.Bool,
+ // `Test if the current atom is part of an secondary structure. Optionally specify allowed sec. struct. types: ${Type.oneOfValues(Struct.Types.SecondaryStructureFlag).join(', ')}`),
+ // args => B.core.flags.hasAny([B.struct.atomProperty.macromolecular.secondaryStructureFlags(), B.struct.type.secondaryStructureFlags(args)])),
+ ],
+ [
+ 'Bond Properties',
+ Alias(MolScript.structureQuery.bondProperty.order, 'bond.order'),
+ // Macro(MSymbol('bond.is', Arguments.List(Struct.Types.BondFlag), Type.Bool,
+ // `Test if the current bond has at least one (or all if partial = false) of the specified flags: ${Type.oneOfValues(Struct.Types.BondFlag).join(', ')}`),
+ // args => B.core.flags.hasAny([B.struct.bondProperty.flags(), B.struct.type.bondFlags(M.getPositionalArgs(args))])),
+ ]
+ ]
+];
+
+const list: MolScriptSymbol[] = [];
+
+function makeList(xs: any[]) {
+ for (const x of xs) {
+ if (isMolScriptSymbol(x)) list.push(x);
+ else if (x instanceof Array) makeList(x);
+ }
+}
+
+makeList(SymbolTable);
+
+const normalized = (function () {
+ const symbolList: [string, MolScriptSymbol][] = [];
+ const symbolMap: { [id: string]: MolScriptSymbol | undefined } = Object.create(null);
+ const namedArgs = UniqueArray.create<string, string>();
+ const constants = UniqueArray.create<string, string>();
+
+ for (const s of list) {
+ for (const a of s.aliases) {
+ symbolList.push([a, s]);
+ if (symbolMap[a]) throw new Error(`Alias '${a}' already in use.`);
+ symbolMap[a] = s;
+ }
+ const args = s.symbol.args;
+ if (args.kind !== 'dictionary') {
+ if (args.type.kind === 'oneof') {
+ Type.oneOfValues(args.type).forEach(v => UniqueArray.add(constants, v, v));
+ }
+ continue;
+ }
+ for (const a of Object.keys(args.map)) {
+ if (isNaN(a as any)) UniqueArray.add(namedArgs, a, a);
+ const arg = ((args.map as any)[a]) as Argument;
+ if (arg.type.kind === 'oneof') {
+ Type.oneOfValues(arg.type).forEach(v => UniqueArray.add(constants, v, v));
+ }
+ }
+ }
+
+ return { symbolList, symbolMap, namedArgs: namedArgs.array, constants: constants.array }
+})();
+
+export const MolScriptSymbols = list;
+export const Constants = normalized.constants;
+export const NamedArgs = normalized.namedArgs;
+export const SymbolMap = normalized.symbolMap;
+export const SymbolList = normalized.symbolList;
+
+function substSymbols(expr: Expression): Expression {
+ if (Expression.isLiteral(expr)) {
+ return expr;
+ }
+ if (Expression.isSymbol(expr)) {
+ if (!SymbolMap[expr.name]) return expr;
+ return Expression.Symbol(SymbolMap[expr.name]!.symbol.id);
+ }
+
+ const head = substSymbols(expr.head);
+ const headChanged = head === expr.head;
+ if (!expr.args) {
+ return headChanged ? Expression.Apply(head) : expr;
+ }
+
+ let argsChanged = false;
+
+ if (Expression.isArgumentsArray(expr.args)) {
+ let newArgs: Expression[] = [];
+ for (let i = 0, _i = expr.args.length; i < _i; i++) {
+ const oldArg = expr.args[i];
+ const newArg = substSymbols(oldArg);
+ if (oldArg !== newArg) argsChanged = true;
+ newArgs[newArgs.length] = newArg;
+ }
+ if (!argsChanged) newArgs = expr.args;
+ if (!headChanged && !argsChanged) return expr;
+ return Expression.Apply(head, newArgs);
+ } else {
+ let newArgs: any = {}
+ for (const key of Object.keys(expr.args)) {
+ const oldArg = expr.args[key];
+ const newArg = substSymbols(oldArg);
+ if (oldArg !== newArg) argsChanged = true;
+ newArgs[key] = newArg;
+ }
+ if (!headChanged && !argsChanged) return expr;
+ if (!argsChanged) newArgs = expr.args;
+
+ return Expression.Apply(head, newArgs);
+ }
+}
-// makeList(SymbolTable);
-
-// const normalized = (function () {
-// const symbolList: [string, MolScriptSymbol][] = [];
-// const symbolMap: { [id: string]: MolScriptSymbol | undefined } = Object.create(null);
-// const namedArgs = UniqueArray.create<string, string>();
-// const constants = UniqueArray.create<string, string>();
-
-// for (const s of list) {
-// for (const a of s.aliases) {
-// symbolList.push([a, s]);
-// if (symbolMap[a]) throw new Error(`Alias '${a}' already in use.`);
-// symbolMap[a] = s;
-// }
-// const args = s.symbol.args;
-// if (args.kind !== 'dictionary') {
-// if (args.type.kind === 'oneof') {
-// Type.oneOfValues(args.type).forEach(v => UniqueArray.add(constants, v, v));
-// }
-// continue;
-// }
-// for (const a of Object.keys(args.map)) {
-// if (isNaN(a as any)) UniqueArray.add(namedArgs, a, a);
-// const arg = ((args.map as any)[a]) as Argument;
-// if (arg.type.kind === 'oneof') {
-// Type.oneOfValues(arg.type).forEach(v => UniqueArray.add(constants, v, v));
-// }
-// }
-// }
-
-// return { symbolList, symbolMap, namedArgs: namedArgs.array, constants: constants.array }
-// })();
-
-// export const MolScriptSymbols = list;
-// export const Constants = normalized.constants;
-// export const NamedArgs = normalized.namedArgs;
-// export const SymbolMap = normalized.symbolMap;
-// export const SymbolList = normalized.symbolList;
+export function transpileMolScript(expr: Expression) {
+ return substSymbols(expr);
+}
// const sortedSymbols = SymbolList.map(s => s[0]).sort((a, b) => {
// if (a.length === b.length) return (a < b) as any;
// return a.length - b.length;
// });
-// export default [...sortedSymbols, ...NamedArgs.map(a => ':' + a), ...Constants];
\ No newline at end of file
+//export default [...sortedSymbols, ...NamedArgs.map(a => ':' + a), ...Constants];
\ No newline at end of file
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index dd0fcdbe0d698c24ad15608659277b5eae45a13c..0329847e96a45993edd765f51830b29dedba7cae 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -6,6 +6,8 @@ import { CustomPropSymbol } from 'mol-script/language/symbol';
import Type from 'mol-script/language/type';
import { parseMolScript } from 'mol-script/language/parser';
import * as util from 'util'
+import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
+import { formatMolScript } from 'mol-script/language/expression-formatter';
// import Examples from 'mol-script/script/mol-script/examples'
// import { parseMolScript } from 'mol-script/script/mol-script/parser'
@@ -15,14 +17,25 @@ import * as util from 'util'
// const expr = parseMolScript(e.value)[0];
// console.log(e.name, util.inspect(expr, true, 10, true));
// }
+// const exprs = parseMolScript(`(sel.atom.atom-groups
+// :residue-test (= atom.auth_comp_id ALA)
+// ;; ho ho ho
+// :atom-test (set.has { _C _N } atom.el)) ; comm
+// ;; this is a comment
+// ((hi) (ho))`);
+
const exprs = parseMolScript(`(sel.atom.atom-groups
- :residue-test (= atom.auth_comp_id ALA)
- ;; ho ho ho
- :atom-test (set.has { _C _N } atom.el)) ; comm
- ;; this is a comment
- ((hi) (ho))`);
+ :residue-test (= atom.label_comp_id REA)
+ :atom-test (= atom.el _C))`);
+
+const tsp = transpileMolScript(exprs[0]);
+
+//console.log(util.inspect(exprs, true, 10, true));
-console.log(util.inspect(exprs, true, 10, true));
+console.log(util.inspect(tsp, true, 10, true));
+
+console.log(formatMolScript);
+console.log(formatMolScript(tsp));
// //console.log(expr);
const expr = MolScriptBuilder.core.math.add([1, 2, 3]);
@@ -49,7 +62,7 @@ export async function testQ() {
const frame = await readCifFile('e:/test/quick/1cbs_updated.cif');
const { structure } = await getModelsAndStructure(frame);
- const expr = MolScriptBuilder.struct.generator.atomGroups({
+ let expr = MolScriptBuilder.struct.generator.atomGroups({
'atom-test': MolScriptBuilder.core.rel.eq([
MolScriptBuilder.struct.atomProperty.core.elementSymbol(),
MolScriptBuilder.es('C')
@@ -61,10 +74,12 @@ export async function testQ() {
'residue-test': MolScriptBuilder.core.rel.inRange([CustomProp.symbols.residueIndex.symbol(), 1, 5])
});
+ expr = tsp;
+
const compiled = compile<StructureQuery>(expr);
const result = compiled(new QueryContext(structure));
console.log(result);
}
-// testQ();
\ No newline at end of file
+testQ();
\ No newline at end of file